Alignments for a candidate for xylA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylA in Azospirillum brasilense Sp245

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate AZOBR_RS27920 AZOBR_RS27920 xylose isomerase

Query= reanno::BFirm:BPHYT_RS32825
         (440 letters)



>FitnessBrowser__azobra:AZOBR_RS27920
          Length = 435

 Score =  573 bits (1477), Expect = e-168
 Identities = 270/435 (62%), Positives = 331/435 (76%), Gaps = 3/435 (0%)

Query: 2   SYFEHIPEIRYEGPQSDNPLAYRHYDKSKKVLGKTLEEHLRIAVCYWHTFVWPGVDIFGQ 61
           +YF  +  IRYEGP SD PLAYR YD  + VLG+ + +HLR+AVCYWH+F WPG D FG 
Sbjct: 4   AYFTGVERIRYEGPDSDTPLAYRWYDPDRMVLGRRMADHLRVAVCYWHSFCWPGSDPFGG 63

Query: 62  GTFRRPWQQAGDAMERAQQKADSAFEFFSKLGTPYYTFHDTDVSPEGSNLKEYSENFLRI 121
           GT  RPW +AGD +  A+ K D AFE F KLG P++TFHD DV+PE  +L+E    F R+
Sbjct: 64  GTLDRPWMRAGDPVALAEAKMDVAFELFGKLGVPFFTFHDRDVAPEMGSLRETQATFARL 123

Query: 122 TDYLARKQESTGIKLLWGTANLFSHPRYAAGAATSPDPEVFAFAATQVRHALDATQRLGG 181
           T+ L    E +G+KLLWGTANLFSHPRY AGAAT+PDPEVFA AA QVR AL+AT RLGG
Sbjct: 124 TERLQGCIERSGVKLLWGTANLFSHPRYMAGAATNPDPEVFACAAAQVRDALEATHRLGG 183

Query: 182 DNYVLWGGREGYDTLLNTDLVRERDQLARFLHMVVDHAHKIGFKGSLLIEPKPQEPTKHQ 241
            NYVLWGGREGYDTLLNTD+ RE DQL RFL MVV+H HKIGF G++LIEPKP EPTKHQ
Sbjct: 184 VNYVLWGGREGYDTLLNTDMARELDQLGRFLTMVVEHKHKIGFTGTILIEPKPMEPTKHQ 243

Query: 242 YDYDVATVHGFLLQHGLDKEIRVNIEANHATLAGHSFHHEIATAYALGIFGSVDANRGDP 301
           YD+DVATV+GFL ++GL+KE+ VNIE NHATLAGHSF HE+ATA ALG+FGS+D NRGDP
Sbjct: 244 YDHDVATVYGFLKRYGLEKEVAVNIEVNHATLAGHSFEHEVATALALGVFGSIDMNRGDP 303

Query: 302 QNGWDTDQFPNSVEELTLAFYEILKHGGFTTGGMNFDSKVRRQSVDPEDLFYGHIGAIDN 361
           QNGWDTDQFPN   EL L    IL+ GGFTTGG NFD+K+RRQSV+P+DL + H+G ID 
Sbjct: 304 QNGWDTDQFPNDHVELALPMARILESGGFTTGGFNFDAKIRRQSVEPDDLLHAHVGGIDT 363

Query: 362 LALAVERAAVLIENDRLDQFKRQRYSGWDAEFGRKISSGDYSLSALAEEAMARGLNPQHA 421
           LA A+   A L+E+ RL   + +RY+GW  + G+K+  G   L+  A+  +  G +P+  
Sbjct: 364 LARALLAGARLVEDGRLRSLRAERYAGWKGDLGQKLLGG-LDLAGAADAGL--GFDPRPR 420

Query: 422 SGHQELMENIVNQAI 436
           SG QE++EN+VN+ +
Sbjct: 421 SGRQEMLENLVNRLV 435


Lambda     K      H
   0.319    0.136    0.414 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 705
Number of extensions: 26
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 440
Length of database: 435
Length adjustment: 32
Effective length of query: 408
Effective length of database: 403
Effective search space:   164424
Effective search space used:   164424
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate AZOBR_RS27920 AZOBR_RS27920 (xylose isomerase)
to HMM TIGR02630 (xylA: xylose isomerase (EC 5.3.1.5))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02630.hmm
# target sequence database:        /tmp/gapView.814161.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02630  [M=435]
Accession:   TIGR02630
Description: xylose_isom_A: xylose isomerase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-198  646.5   0.0   1.2e-198  646.3   0.0    1.0  1  FitnessBrowser__azobra:AZOBR_RS27920  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__azobra:AZOBR_RS27920  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  646.3   0.0  1.2e-198  1.2e-198       1     434 [.       5     434 ..       5     435 .] 0.98

  Alignments for each domain:
  == domain 1  score: 646.3 bits;  conditional E-value: 1.2e-198
                             TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdkeltda 73 
                                           +f+++e+++yeG+ds+ pla+++y+p++++ g++m dhlr av+yWh++++ g+DpfG+gt +rpw  +  d+
  FitnessBrowser__azobra:AZOBR_RS27920   5 YFTGVERIRYEGPDSDTPLAYRWYDPDRMVLGRRMADHLRVAVCYWHSFCWPGSDPFGGGTLDRPWM-RAGDP 76 
                                           89****************************************************************9.57*** PP

                             TIGR02630  74 ldkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWgtanlfshp 146
                                           ++ a+ak+d+afel+ klgv++++fhD+D+ape  sl+et+a++ ++++ l+   +++gvklLWgtanlfshp
  FitnessBrowser__azobra:AZOBR_RS27920  77 VALAEAKMDVAFELFGKLGVPFFTFHDRDVAPEMGSLRETQATFARLTERLQGCIERSGVKLLWGTANLFSHP 149
                                           ************************************************************************* PP

                             TIGR02630 147 ryvaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnlarflklavdyak 219
                                           ry+aGaat+pd++vfa aaaqv+ ale+t++lgg nyv+WGGreGy+tLlntd+++eld+l+rfl+++v++++
  FitnessBrowser__azobra:AZOBR_RS27920 150 RYMAGAATNPDPEVFACAAAQVRDALEATHRLGGVNYVLWGGREGYDTLLNTDMARELDQLGRFLTMVVEHKH 222
                                           ************************************************************************* PP

                             TIGR02630 220 kigfkgqlliePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaghtfehelrvarelgllGs 292
                                           kigf+g++liePkP+ePtkhqyD D+atv++flk+y+L+k++ +nie+nhatLagh+fehe+++a +lg++Gs
  FitnessBrowser__azobra:AZOBR_RS27920 223 KIGFTGTILIEPKPMEPTKHQYDHDVATVYGFLKRYGLEKEVAVNIEVNHATLAGHSFEHEVATALALGVFGS 295
                                           ************************************************************************* PP

                             TIGR02630 293 iDanrgdlllGWDtDefptdvyeatlamyevlkagglakGGlnfdakvrresldaeDlllahiagmDafargl 365
                                           iD+nrgd ++GWDtD+fp+d  e++l m ++l++gg+++GG+nfdak+rr+s++++Dll+ah++g+D++ar+l
  FitnessBrowser__azobra:AZOBR_RS27920 296 IDMNRGDPQNGWDTDQFPNDHVELALPMARILESGGFTTGGFNFDAKIRRQSVEPDDLLHAHVGGIDTLARAL 368
                                           ************************************************************************* PP

                             TIGR02630 366 kvaaklledgaleklveeryesfdseiGkeieegkadleelekyalekeeeaekksgrqelleslinky 434
                                            + a+l+edg+l +l +ery++++ ++G++++ g  dl+  ++  l    +++ +sgrqe+le+l+n+ 
  FitnessBrowser__azobra:AZOBR_RS27920 369 LAGARLVEDGRLRSLRAERYAGWKGDLGQKLLGG-LDLAGAADAGLGF--DPRPRSGRQEMLENLVNRL 434
                                           ********************************98.8888888877666..68***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (435 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 28.42
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources